On Mon, May 30, 2016, Shreeramesh wrote:
>
> I have to run MD simulation in AMBER for the protein-DNA system comprising
> magnesium ion.
>
> Can you please guide me how to treat magnesium ion in the complex?
Please see the "ions" section in section 3.6 of the Amber 2016 Reference
Manual. The parameters for ions are tightly coupled with which water model
you choose. In AmberTools16, we have simplified things quite a bit: if you
choose a water model (by loading a leaprc.water.* file), you automatically get
our recommended parameters for monatomic ions.
Aside: divalent ions are difficult to simulation, so advanced users may wish
to explore other combinations of parameters.
...good luck....dac
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Received on Mon May 30 2016 - 06:30:03 PDT
